IMHO, for me, none of the eBook reader devices (ePaper or similar) offer easy and trusted workflow of PDF annotations, highlights and syncing them properly. Most are kludgy, proprietary and unreliable.

The easiest and most expensive way is just to get an iPad and buy a proper PDF management, marking, indexing and searching app like Papers.

A similar one for Android seems to be Mantano eBook reader, althought not anywhere near as comprehensive.

YMMV, of course.

I agree with you on the first part. I too havent found eInk reader that is really good with pdf. The reason for this is simply screen size. Let's face it, 6' screen is just bad for pdf. And highlighting is not so simple, as well as making notes, annotations, drawings and so on.

As for getting the iPad just to read the pdfs? Sheer stupidity. It might be the easiest way, but lets face it. If you are a student and not some 60 yo housewife, you should give yourself some credit and try other tablet options out there. What I mean is I expect a student to be little bit more tech savy then an average housewife and give the android market a go. Plus the customizability. Oh the customization is best part. Why confine yourself with iOS. Yuck.

Now, I'm a student and my choice was same as OP's. I had to find something to mainly read pdf on with ability to take notes. I knew most important thing would be screen size. So I went with 10' tablet. That's the only thing that matters with pdf really. My choice was Lenovo ThinkPad Tablet. The specs are in the attachments. Price? 322$ compared to iPad 546$ with same 32 GB model. (prices in Japan).
Bonus thing is Lenovo tablet has a real stylus pen. So I can make annotations and highlights like I would with marker on a paper book.

As for annotations I tried a lot of applications, but I stick with ezPDF Reader now. Its perfect for highlight and notations. Its not expensive; google store has it.

The point is, buying a iPad to read Pdf is madness. Give an android tablet a try. There is plenty of good tablets from Lenovo, Samsung, Sony. Don't spend more then 500$ because that's an easy way out. Do your research. You're a student aren't you?